Diatom valves and girdle bands are useful micro-nano materials in nanotechnology and micro manufacturing. A settling method is used to extract high-purity diatom valves and girdle bands from Coscinodiscus diatomite. The average models of diatom valves and girdle bands are established. Stokes Law and hydrokinetic theories are used to analyze the settling velocity of valves and girdle bands. Based on the calculation results, settling experiments are carried out, by which clean diatom valves with purity of 80% and girdle bands with purity of 90% are obtained. This method can be applied to other particles separation problem to separate micro-particles with similar radius but different sectional area.